Despite dominating the majority of the game at Beath High School we went down to a second successive defeat.
The young blues opened the game brightly and almost opened the scoring after just three minutes when Finnie sent a long ball to Gill who fired a cross into the Dundee box with Nicholson just unable to connect to the ball.
Minutes later they came even closer when Callaghan sent a deep free kick into the visitor’s box which Nicholson touched onto the post with the ball bouncing into the hands of keeper Johnstone.
In a rare Dundee attack McLeod headed wide of the post but with 34 minutes gone they took the lead against the run of play.
Finnie was judged to have fouled McLeod in the box and Rory Bewes slotted home the resultant spot kick.
The start of the second half once again saw Cowden enjoy the majority of the play and keeper Johnstone done well to block a shot for Milne.
However, once again the Dee proved to be the more clinical finishers when they added a second goal after 65 minutes with Greg Birmingham taking advantage of slack defending to shoot home from the edge of the box.
Eight minutes later Birmingham grabbed his second goal of the afternoon when he sent a low shot past the diving Wilson from just inside the box.
A Dundee win appeared to be on the cards but the Cowden youngsters showed their battling qualities and a dipping shot from Nicholson from 25 yards went just over the bar.
With 11 minutes left on the clock they however eventually breached the Dundee goal with Lewis Milne heading home from eight yards.
Sensing a comeback they bombarded the visiting goal and got a second goal with two minutes remaining with Jack Nicholson heading home from a Pyper cross.
Any hopes of salvaging a point however were dashed as Dundee held out to claim the points.